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Characterization of a Cell Death Suppressing Effector Broadly Conserved Across the Fungal Kingdom Ehren Lee Whigham Iowa State University

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Characterization of a Cell Death Suppressing Effector Broadly Conserved Across the Fungal Kingdom Ehren Lee Whigham Iowa State University Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2013 Characterization of a cell death suppressing effector broadly conserved across the fungal kingdom Ehren Lee Whigham Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Agricultural Science Commons, Agriculture Commons, and the Plant Pathology Commons Recommended Citation Whigham, Ehren Lee, "Characterization of a cell death suppressing effector broadly conserved across the fungal kingdom" (2013). Graduate Theses and Dissertations. 13431. https://lib.dr.iastate.edu/etd/13431 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Characterization of a cell death suppressing effector broadly conserved across the fungal kingdom by Ehren L. Whigham A thesis submitted to the graduate faculty in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Major: Plant Pathology Program of Study Committee: Roger P. Wise, Major Professor Adam Bogdanove Erik Vollbrecht Iowa State University Ames, Iowa 2013 Copyright © Ehren L. Whigham, 2013, All rights reserved. ii TABLE OF CONTENTS GLOSSARY/ABBREVIATIONS .................................................................... iii ABSTRACT .................................................................................................. iv CHAPTER 1 GENERAL INTRODUCTION ............................................... 1 Thesis Organization ................................................................................ 1 Literature Review .................................................................................... 1 References ............................................................................................. 12 CHAPTER 2 AN EFFECTOR BROADLY CONSERVED ACROSS THE FUNGAL KINGDOM SUPPRESSES CELL DEATH ............................ 17 Introduction ............................................................................................. 17 Results ............................................................................................. 19 Discussion ............................................................................................. 35 Materials and Methods ............................................................................ 39 Acknowledgements ................................................................................. 47 Author Contributions ............................................................................... 47 References ............................................................................................. 47 CHAPTER 3 ITAG BARLEY: A 9-12 CLASSROOM MODULE TO EXPLORE GENE EXPRESSION AND SEGREGATION USING OREGON WOLFE BARLEY ......................................................................... 53 Overview of the project ........................................................................... 53 The learning module ............................................................................... 58 Extensions to the module ........................................................................ 66 Appendices ............................................................................................. 77 Acknowledgements ................................................................................. 84 CHAPTER 4 CONCLUSIONS AND FUTURE DIRECTIONS ................... 86 Conclusions ............................................................................................ 86 Future Directions ..................................................................................... 87 References .............................................................................................. 88 APPENDIX SUPPLEMENTAL DATA FOR CHAPTER 2 ........................... 90 Supplemental Figure 1 ......................................................................... 90 Supplemental Figure 2 ......................................................................... 91 Supplemental Table 1 .......................................................................... 92 Supplemental Table 2 .......................................................................... 96 Supplemental Table 3 .......................................................................... 100 Supplemental Table 4 .......................................................................... 103 iii GLOSSARY/ABBREVIATIONS PAMP Pathogen Associated Molecular Pattern PTI PAMP-triggered Immunity Effector Defined in this thesis as pathogen proteins and small molecules that modify host defense ETI Effector-triggered Immunity R-gene Resistance gene Avr-gene Avirulence gene BEC Blumeria effector candidate RNAi RNA interference; Eukaryotic viral defense mechanism to digest double stranded RNA HIGS Host-Induced Gene Silencing; a transient, single-cell RNAi mediated gene silencing system BSMV-VIGS Barley Stripe Mosaic Virus-Induced Gene Silencing; a transient, systemic RNAi mediated gene silencing system Type III secretion system Needle-like molecular structure used by some bacteria to deliver proteins into host cells HR Hypersensitive reaction, defined in this thesis as a rapid cell death response at the infection site Homolog Genes sharing a similar DNA sequence due to descent from a common ancestor Ortholog Genes in different species that share a common ancestral DNA sequence as a result of a speciation event; often these genes retain similar functions Paralog Result of gene duplication in a species enabling evolution of gene variants with new functions iv ABSTRACT The proteins used by pathogens to modify, suppress or evade host defenses (called effectors) are fascinating probes into plant defense pathways and are changing the way scientists think about host/pathogen interactions. Blumeria graminis f. sp. hordei, causal agent of barley powdery mildew disease, is a model system to study the nature of obligate biotrophy. In addition to the nearly 500 predicted effector candidates unique to the mildews, this pathogen contains at least one that is broadly conserved across the fungal kingdom. Understanding the functions and targets of both the unique and conserved effectors has the potential to reveal new mechanisms of resistance. The development of RNAi-mediated gene silencing assays and the use of bacterial secretion based delivery systems has enabled the functional characterization of effectors in ways that were impossible until now. Silencing an effector candidate from B. graminis by Barley Stripe Mosaic Virus –Induced Gene Silencing is shown to significantly reduce accumulation of fungal biomass. When delivered to barley cells via the Xanthomonas bacterial type III secretion system, this effector is able to suppress host cell death. Conservation of this protein in 96 of 240 surveyed fungal genomes is presented. Notably, orthologs of this gene are present in non-pathogens as well as major pathogens of both plants and animals. Site-directed mutagenesis revealed two amino acids that are required for the cell death suppression phenotype. Taken together, this evidence supports reclassification of this gene from candidate effector to bona fide effector. Biological research and bioinformatic analysis are meaningful only to the extent that scientists can communicate value to stakeholders and the public. Through collaboration with high school science teachers, a curriculum was developed to expose students to plant biology and illustrate that an organism’s DNA (genotype) has a direct influence on its traits (phenotype). Students plant seeds, extract DNA from leaf tissue, amplify genes through polymerase chain v reactions, and screen plant phenotypes. They learn to use pipets, how to conduct PCR and gel electrophoresis, and spend time determining relevant traits of their plants. The goal is to equip teachers to train and excite students about the field of plant biology. 1 CHAPTER 1: GENERAL INTRODUCTION Thesis Organization The focus of this thesis is the characterization of Blumeria Effector Candidate (BEC) 1019. A literature review detailing the history of effector biology is presented in the first chapter. Topics include Flor’s study of flax which led to the gene-for-gene hypothesis, the bacterial type III secretion system and its effectors, identification of the first filamentous fungal effectors, sequencing of the Blumeria graminis f. sp. hordei genome, detailed annotation, and the first functional screen of B. graminis effectors. The second chapter is a manuscript to be submitted to PLOS Pathogens describing functional analysis of BEC1019 through the use of systemic Virus-induced gene silencing (VIGS) and the Xanthomonas type III secretion system for protein delivery into host cells. The third chapter is a curriculum written in collaboration with several Iowa State University Research Experience for Teachers (ISU-RET) interns that has been published on the American Society of Plant Biologists education website. The final chapter lists general conclusions and future directions for the study of BEC1019. Literature Review Introduction The increasing global population is forcing the agriculture industry to produce more food, fuel and fiber on less land. Past approaches to addressing this issue include breeding for desired
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